SCOPe 2.03: Structural Classification of Proteins

PDB entry 2ja8

View 2ja8 on RCSB PDB site
Description: cpd lesion containing RNA polymerase II elongation complex d
Class: transferase
Keywords: DNA-directed RNA polymerase, lesion recognition, transferase/DNA/RNA, DNA damage, zinc-finger, DNA-binding, photolesion, phosphorylation, misincorporation, RNA polymerase II, transcription-coupled repair, cyclobutane pyrimidine dimer tcr, cpd, zinc, arrest, stalling, DNA lesion, metal-binding, nuclear protein, transcription bubble, nucleotidyltransferase, damage recognition, elongation complex, transferase, thymine dimer, transcription
Deposited on 2006-11-23, released 2007-02-20
The last revision prior to the SCOPe 2.03 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 3.8 Å
R-factor: 0.2686
AEROSPACI score: 0.06 (click here for full SPACI score report)

Chains and heterogens:

Chain 'A':
Compound: DNA-directed RNA polymerase II largest subunit
Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P04050
Domains in SCOPe 2.03: d2ja8a1
Chain 'B':
Compound: DNA-directed RNA polymerase II 140 kDa polypeptide
Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P08518 (Start-1223)
Domains in SCOPe 2.03: d2ja8b1
Chain 'C':
Compound: DNA-directed RNA polymerase II 45kda polypeptide
Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P16370
Domains in SCOPe 2.03: d2ja8c1, d2ja8c2
Chain 'D':
Compound: DNA-directed RNA polymerase II 32kda polypeptide
Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P20433 (Start-220)
Domains in SCOPe 2.03: d2ja8d1
Chain 'E':
Compound: DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P20434 (Start-214)
Domains in SCOPe 2.03: d2ja8e1, d2ja8e2
Chain 'F':
Compound: DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P20435 (Start-154)
Domains in SCOPe 2.03: d2ja8f1
Chain 'G':
Compound: DNA-directed RNA polymerase II 19kda polypeptide
Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P34087 (0-170)
Domains in SCOPe 2.03: d2ja8g1, d2ja8g2
Chain 'H':
Compound: DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P20436 (Start-145)
Domains in SCOPe 2.03: d2ja8h1
Chain 'I':
Compound: DNA-directed RNA polymerase II subunit 9
Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P27999
Domains in SCOPe 2.03: d2ja8i1, d2ja8i2
Chain 'J':
Compound: DNA-directed RNA polymerases I/II/III subunit 10
Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P22139 (0-End)
Domains in SCOPe 2.03: d2ja8j1
Chain 'K':
Compound: DNA-directed RNA polymerase II 13.6 kDa polypeptide
Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P38902 (0-End)
Domains in SCOPe 2.03: d2ja8k1
Chain 'L':
Compound: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
Species: SACCHAROMYCES CEREVISIAE [TaxId:4932]
Database cross-references and differences (RAF-indexed):
- Uniprot P40422 (Start-69)
Domains in SCOPe 2.03: d2ja8l1
Chain 'N':
Compound: 5'-d(*tp*ap*ap*gp*tp*ap*cp*tp*tp*gp *ap*gp*cp*t)-3'
Species: synthetic, synthetic
Chain 'P':
Compound: 5'-r(*up*up*cp*gp*ap*cp*cp*ap*gp*ap*up)-3'
Species: synthetic, synthetic
Chain 'T':
Compound: 5'-d(*ap*gp*cp*tp*cp*ap*ap*gp*tp*ap *cp*tp*tp*tp*tp*ttp*cp*brup*gp*gp*tp*cp*ap*tp*t)-3'
Species: synthetic, synthetic
Heterogens: MG, ZN

PDB Chain Sequences:

Chain 'A':
Sequence, based on SEQRES records: (download)

>2ja8A (A:)
mvgqqyssaplrtvkevqfglfspeevraisvakirfpetmdetqtrakigglndprlgs
idrnlkcqtcqegmnecpghfghidlakpvfhvgfiakikkvcecvcmhcgkllldehne
lmrqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqptirkdglk
lvgswkkdratgdadepelrvlsteeilnifkhisvkdftslgfnevfsrpewmiltclp
vppppvrpsisfnesqrgeddltfkladilkanisletlehngaphhaieeaesllqfhv
atymdndiagqpqalqksgrpvksirarlkgkegrirgnlmgkrvdfsartvisgdpnle
ldqvgvpksiaktltypevvtpynidrltqlvrngpnehpgakyvirdsgdridlryskr
agdiqlqygwkverhimdndpvlfnrqpslhkmsmmahrvkvipystfrlnlsvtspyna
dfdgdemnlhvpqseetraelsqlcavplqivspqsnkpcmgivqdtlcgirkltlrdtf
ieldqvlnmlywvpdwdgviptpaiikpkplwsgkqilsvaipngihlqrfdegttllsp
kdngmliidgqiifgvvekktvgssngglihvvtrekgpqvcaklfgniqkvvnfwllhn
gfstgigdtiadgptmreitetiaeakkkvldvtkeaqanlltakhgmtlresfednvvr
flneardkagrlaevnlkdlnnvkqmvmagskgsfiniaqmsacvgqqsvegkriafgfv
drtlphfskddyspeskgfvensylrgltpqefffhamggreglidtavktaetgyiqrr
lvkaledimvhydnttrnslgnviqfiygedgmdaahiekqsldtiggsdaafekryrvd
llntdhtldpsllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvni
rriiqnaqqtfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlfcc
llrsrlatrrvlqeyrltkqafdwvlsnieaqflrsvvhpgemvgvlaaqsigepatqmt
lntfhfagvaskkvtsgvprlkeilnvaknmktpsltvylepghaadqeqaklirsaieh
ttlksvtiaseiyydpdprstvipedeeiiqlhfslldeeaeqsfdqqspwllrleldra
amndkdltmgqvgerikqtfkndlfviwsedndekliircrvvrpksldaeteaeedhml
kkientmlenitlrgveniervvmmkydrkvpsptgeyvkepewvletdgvnlsevmtvp
gidptriytnsfidimevlgieagraalykevynviasdgsyvnyrhmallvdvmttqgg
ltsvtrhgfnrsntgalmrcsfeetveilfeagasaelddcrgvsenvilgqmapigtga
fdvmideeslvkympeqkiteiedgqdggvtpysnesglvnadldvkdelmfsplvdsgs
ndamaggftayggadygeatspfgaygeaptspgfgvsspgfsptsptysptspayspts
psysptspsysptspsysptspsysptspsysptspsysptspsysptspsysptspsys
ptspsysptspsysptspsysptspsysptspsysptspaysptspsysptspsysptsp
sysptspsysptspnysptspsysptspgyspgspayspkqdeqkhnenensr